from pathlib import Path

from ipyniivue import download_dataset

BASE_API_URL = "https://niivue.com/demos/images/"
DATA_FOLDER = Path("images")

# Download data for example
download_dataset(
    BASE_API_URL,
    DATA_FOLDER,
    files=[
        "mni152.nii.gz",
        "BrainMesh_ICBM152.lh.mz3",
        "dpsv.trx",
        "connectome.jcon",
    ],
)

mni152.nii.gz already exists.
BrainMesh_ICBM152.lh.mz3 already exists.
dpsv.trx already exists.
connectome.jcon already exists.
Dataset downloaded successfully to images.

import ipywidgets as widgets
from IPython.display import display

from ipyniivue import NiiVue

## Initialize Viewer
nv = NiiVue()

nv.load_volumes([{"path": DATA_FOLDER / "mni152.nii.gz"}])
nv.load_meshes(
    [
        {
            "path": DATA_FOLDER / "BrainMesh_ICBM152.lh.mz3",
            "rgba255": [255, 64, 32, 255],
        },
        {"path": DATA_FOLDER / "dpsv.trx"},
        {"path": DATA_FOLDER / "connectome.jcon"},
    ]
)

nv.set_mesh_shader(nv.meshes[0].id, "crosscut")
nv.set_clip_plane(-0.1, 270, 0)
nv.opts.mesh_xray = 0.02

## Create Interactive Controls

edge_slider = widgets.IntSlider(
    value=10, min=5, max=30, description="Edge", readout=False
)


def on_edge_change(change):
    """Set edge diameter."""
    nv.set_mesh_property(nv.meshes[2].id, "edge_scale", change["new"] * 0.1)


edge_slider.observe(on_edge_change, names="value")

node_slider = widgets.IntSlider(
    value=10, min=5, max=30, description="Node", readout=False
)


def on_node_change(change):
    """Set node diameter."""
    nv.set_mesh_property(nv.meshes[2].id, "node_scale", change["new"] * 0.1)


node_slider.observe(on_node_change, names="value")

## Display Viewer

controls = widgets.HBox([edge_slider, node_slider])

display(controls)
display(nv)

Voxels, meshes, streamlines, and connectomes¶